DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Application Status
Applicant’s remarks, and amendments to the claims filed June 1, 2026 are acknowledged. Claims 35, 42, and 49 were amended, and claims 55-56 were cancelled. Claims 35, 39-44, and 46-54 are pending and under examination herein.
Withdrawn Rejections
The amendments to the claims overcome the § 112(d) and § 112(b) rejections of claims 55-56 raised in the prior action. These rejections are withdrawn. The remaining § 112(b) rejections raised in the prior action are withdrawn in view of Applicant’s remarks, which argue convincingly that a lysis means disclosed in the specification, i.e., sonication, would not result in the complete destruction of all DNA contained in all of the cells used to prepare the whole cell lysate. The structure of the whole cell lysate is sufficiently definite, as further detailed in the claim interpretation below.
Applicant’s remarks and amendments to the claims have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow. Any rejection or objection not reiterated herein has been overcome by amendment.
Claim Interpretation
Claim 35 is directed to a “whole cell lysate.” The term “whole cell lysate” is not explicitly defined in the specification, and is interpreted hereinafter as referring to as a product produced by lysing whole cells. The whole cell lysate is a product-by-process. MPEP 2113 (I) states that “product-by-process claims are not limited to the manipulations of the recited steps, only the structure implied by the steps.”
The claim recites that the lysate is “prepared from a high-growth capacity, auxotrophic strain of E. coli cells, wherein… the doubling rate of a population of cells of the auxotrophic strain of E. coli is less than 60 minutes in a growth media comprising glutamine.” However, the E. coli cells from which the lysate is prepared are not required to be cultured under any particular conditions, so while the auxotrophic strain of E. coli is “high-growth capacity” (emphasis added), and a population of the E. coli cells has a “doubling rate of… less than 60 minutes in a growth media comprising glutamine,” these properties do not limit the structure of the whole cell lysate. This conclusion is supported by evidence in the specification, cited in the prior actions, which demonstrates that similar assembled IgG titers were produced from bacterial cell extracts prepared from “high-growth capacity” auxotrophic glnA-deficient E. coli cells comprising a complementing plasmid (i.e., the recited E. coli cells), and equivalent non-auxotrophic cells ([0071]; [0135]; [0139]-[0140]; Fig. 6).
The claim also recites that the auxotrophic E. coli cells from which the lysate is prepared I) “comprise[] an inactivated gene necessary for glutamine synthesis,” and II) “comprise an auxotrophic selection plasmid having an expression cassette comprising a constitutive promoter operably linked to a glnA gene.” The means to prepare the lysate are not limited. The skilled artisan would know that DNA may be fragmented and/or degraded in the process of preparing a whole cell lysate, e.g., during sonication, or when using a lysis buffer containing nuclease. Thus, a whole cell lysate of the auxotrophic E. coli cells would not necessarily comprise a complete “inactivated gene necessary for glutamine synthesis,” or “expression cassette comprising a constitutive promoter operably linked to a glnA gene,” and could, for example, comprise fragments thereof.
Taken together, the whole cell lysate is interpreted as a mixture of E. coli cell contents wherein the mixture comprises at least a fragment of (i.e., two or more consecutive nucleotides of) an inactivated gene necessary for glutamine synthesis, and at least a fragment of an expression cassette comprising a constitutive promoter operably linked to a glnA gene.
Notice to Joint Inventors
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim Rejections - 35 USC § 103 – Yin in view of Dong
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 35, 40-44, and 47-54 are rejected under 35 U.S.C. 103 as being unpatentable over Yin (Yin et al., 1 March 2012, Landes Bioscience, mAbs, 4:2, p. 217-225; of record) as evidenced by Zawada (Zawada et al., 17 February 2011, Biotechnology and Bioengineering, Vol. 108, Issue 7, and Supporting Materials; of record), in view of Dong (Dong et al., April 2010, Applied and Environmental Microbiology, p. 2295-2303; of record). The rejections that follow are maintained with revisions to clarify the rationale in view of Applicant’s cancellation of claim 56 (the structural limitations of which were used to interpret the claims in the prior action), and persuasive remarks regarding the structure of the whole cell lysate, and to address the claim interpretation above, necessitated thereby.
Regarding claim 35, Yin teaches a whole cell lysate (the cell extract for the “open cell-free synthesis (OCFS) system”), which as evidenced by Zawada, was prepared by lysing whole E. coli cells (“Cell extracts were prepared using a previously engineered K-12-dervied E. coli strain… cells were lysed in a homogenizer,” pg. 1571). See Yin, pg. 222, which states that the methodology used was as described in Zawada (“The previously described high copy T7-based plasmid pYD31719, used for all plasmids in this work,” pg. 222, left col.; “The cell-free reactions were run... as previously described in reference 19,” pg. 222, right col.).
Yin teaches the lysate comprises a plasmid (“pYD317”) comprising a template nucleic acid comprising a gene of interest (“scFV”, “Fab”, and “trastuzumab IgG1”) operably linked to at least one promoter (“T7 promoter”)(“T7 plasmid design,” pg. 222; “cell extract is mixed with template DNA (plasmid”, pg. 218). Yin teaches the plasmid comprises a kanamycin resistance gene linked to a T7 promoter, which is a constitutive promoter (pg. 222, left col.). Zawada teaches that “large-scale production of [pYD317] plasmid DNA” from transformed E. coli precedes the cell-free synthesis reactions (see pgs. 2-3 of Supporting Materials; pg. 1571, “Gene Expression Constructs” and “OCFS Protein Synthesis Reaction Conditions”).
Yin as evidenced by Zawada does not teach that the lysate comprises at least a fragment of (i.e., two or more consecutive nucleotides of) an inactivated gene necessary for glutamine synthesis, and at least a fragment of an expression cassette comprising a constitutive promoter operably linked to a glnA gene.
However, Dong teaches that while antibiotic resistance genes are the “most commonly used markers for selecting and maintaining recombinant plasmids in hosts, such as Escherichia coli… the use of these genes has several drawbacks” (pg. 2295, left col.). These drawbacks include “horizontal transfer of the antibiotic resistance gene [] potentially contribut[ing] to the rapid emergence of multidrug-resistant organisms,” “antibiotics [] cost[] in large-scale cultivation, and [] risks of contamination of the final product with antibiotics,” and the “metabolic burden on host cells” “constitutively express[ing] antibiotic resistance genes,” “resulting in reduced growth rate and cell density” (pg. 2295, left col.). Dong teaches that an alternative to antibiotic resistance is auxotrophic complementation, in which an auxotrophic strain for an essential metabolite is “obtained by mutating or knocking out the corresponding chromosomal gene, which can be complemented with the plasmid-borne selection gene” (pg. 2295, right col.). Dong teaches essential genes that have been utilized to construct auxotrophic selection systems, including “glnA” (pg. 2295, right col.).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted antibiotic selection in the plasmid of Yin, for auxotrophic selection using the glnA gene taught by Dong, to arrive at the whole cell lysate of claim 35 as interpreted herein. It would have amounted to a simple substitution of two known selection methods, by known means to yield predictable results. The skilled artisan would have had reasonable expectation of success in mutating or knocking out the chromosomal glnA gene in Yin’s E. coli, and substituting the kanamycin resistance gene in Yin’s plasmid with a glnA gene, because Dong teaches that auxotrophic selection systems based on glnA knockout and complementation have been utilized, and as evidenced by Yin and Dong, it was well within the purview of the skilled artisan to prepare E. coli deficient in specific genes, and recombinant plasmids with sequences of interest. The skilled artisan would have recognized the potential advantages of Dong’s auxotrophic selection method for the “large-scale production of plasmid DNA” in the method of Yin as evidenced by Zawada, and therefore, would have been motivated to substitute Yin’s and Dong’s selection methods.
Regarding claims 40-41, Yin teaches the lysate further comprises a chaperone protein, wherein the chaperone protein is DsbC (“we co-expressed the HC and LC of trastuzumab, in the presence of added disulfide isomerase chaperones DsbC or PDI”, pg. 220; Cell-free reactions, pg. 222).
Regarding claim 42, the inactivated gene rendered obvious above is glnA. This claim is also obvious over the prior art above.
Regarding claim 43, Yin teaches a reaction mixture comprising the whole cell lysate and a template nucleic acid comprising a gene of interest (“scFV”, “Fab”, and “trastuzumab IgG1”) operably linked to at least one promoter (“T7 promoter”) (T7 plasmid design, pg. 222; “cell extract is mixed with template DNA”, pg. 218; “addition of… individual HC and LC T7-based plasmids”, Fig. 1 description).
Regarding claim 44, Yin teaches the reaction mixture further comprises an RNA polymerase that recognizes the promoter operably linked to the gene of interest (“The cell extract is mixed with… T7 RNA polymerase (RNAP)”, pg. 218; “Addition of T7-RNA polymerase (RNAP), individual HC and LC T7-based plasmids… drives transcription and subsequent ribosomal translation”, Fig. 1 description).
Regarding claims 47-48, Yin teaches the reaction mixture further comprises a chaperone protein, wherein the chaperone protein is DsbC (“we co-expressed the HC and LC of trastuzumab, in the presence of added disulfide isomerase chaperones DsbC or PDI”, pg. 220; Cell-free reactions, pg. 222).
Regarding claim 49, the inactivated gene rendered obvious above is glnA. This claim is also obvious over the prior art above.
Regarding claims 50 and 54, Yin teaches a method for producing a biologically active antibody (“The OCFS system produces antibodies… [which] are fully soluble, non-aggregated, correctly folded, functional in biochemical and cell-based assays”, pg. 221, left col.). Yin teaches the method comprises mixing the whole cell lysate with amino acids, nucleotides, and an energy source (“The cell extract is mixed with… amino acids, nucleotides,… and an energy source”, pg. 218, left col., Fig. 1), as well as template nucleic acid comprising a gene of interest operably linked to at least one promoter (“T7 promoter”) (T7 plasmid design, pg. 222; “The cell extract is mixed with template DNA”, pg. 218, left col.; “addition of… individual HC and LC T7-based plasmids”, Fig. 1 description). Yin teaches conditions sufficient to transcribe the template DNA and translate the resultant mRNA into the protein of interest (Fig. 1 description; Cell-free reactions, pg. 222, Figs. 2-4).
Regarding claims 51-52, Yin teaches the template nucleic acid is DNA comprising an RNA polymerase promoter (“T7 promoter”) (T7 plasmid design, pg. 222; “The cell extract is mixed with template DNA”, pg. 218, left col.; “addition of… individual HC and LC T7-based plasmids”, Fig. 1 description). Yin teaches the lysate comprises an RNA polymerase (“The cell extract is mixed with… T7 RNA polymerase (RNAP)”, pg. 218; “Addition of T7-RNA polymerase (RNAP), individual HC and LC T7-based plasmids… drives transcription and subsequent ribosomal translation”, Fig. 1 description).
Regarding claim 53, Yin teaches the method comprises amino acids, which are interpreted as being within the scope of “natural or non-natural amino acids,” because this phrase encompasses all amino acids.
Claim Rejections - 35 USC § 103 – Yin and Dong in view of Zimmerman
Claims 39 and 46 are rejected under 35 U.S.C. 103 as being unpatentable over Yin (Yin et al., 1 March 2012, Landes Bioscience, mAbs, 4:2, p. 217-225; of record) as evidenced by Zawada (Zawada et al., 17 February 2011, Biotechnology and Bioengineering, Vol. 108, Issue 7, and Supporting Materials; of record) in view of Dong (Dong et al., April 2010, Applied and Environmental Microbiology, p. 2295-2303; of record) as applied to claims 35, 40-44, and 47-54 above, and in further view of Zimmerman (Zimmerman et al., 17 January 2014, Bioconjugate Chemistry, 25, p. 351-361; of record). The rejections that follow are maintained with modification necessitated by Applicant’s amendments.
Claims 39 and 46 recite that the whole cell lysate and reaction mixture “further compris[e] a suppressor tRNA… expressed from the auxotrophic selection plasmid.” The whole cell lysate is a product by process. As such, the claims are interpreted as requiring that the lysate and reaction mixture comprise a suppressor tRNA. A “suppressor tRNA” is interpreted as a tRNA that allows incorporation of a non-natural amino acid (nnAA) into a polypeptide chain in response to a specific codon, e.g., a stop codon, or rare codon ([0042]).
The teachings of Yin, Zawada, and Dong are described above and applied as to claims 35, 40-44, and 47-54 therein.
None of Yin, Zawada, or Dong teach that the lysate and reaction mixture comprise a suppressor tRNA.
Zimmerman teaches an E. coli lysate for use in an open cell-free synthesis (OCFS) system that includes a non-natural amino acid (nnAA) incorporation system comprising a plasmid driving constitutive expression of a suppressor tRNA (“Cell free expression reactions [had] the following modifications… the base extract E. coli strain… was transformed with a plasmid driving constitutive expression of an optimized amber suppressor tRNA… and prepared as an extract”, pg. 352, CF-Based aaRS Screening; pg. 351-352; Cell Free Protein Expression, pg. 353). Zimmerman teaches that recoding of nonproteinogenic codons, e.g., the amber stop codon TAG, enables incorporation of a nnAA at essentially any desired site in a protein (pg. 352, left col.). Zimmerman teaches that nnAAs with reactive side chains serve as a chemical “handle” to conjugate a payload, e.g., a chemotherapeutic agent, to a desired site in the protein (pg. 352, left col.).
Indeed, Zimmerman demonstrates that that an OCFS system comprising the lysate with the suppressor tRNA (“optimized amber suppressor tRNA”), and remaining elements of the nnAA incorporation system, (e.g., the aminoacyl tRNA synthetase “pAMFRS”) can be used to create antibody-drug conjugates (ADCs), e.g., Trastuzumab antibodies conjugated to the chemotherapeutic compound monomethyl auristatin (“DBCO-PEG-monomethyl auristatin (DBCO-PEG-MMAF)”) (Cell Free Protein Expression, pg. 353, left col.; pg. 357, Fig. 4). Zimmerman teaches that while several ADCs are FDA-approved and demonstrate positive clinical performance, the drug conjugation process is typically performed stochastically (e.g., by conjugation to surface-exposed lysines and cysteines) which leads to ADCs with heterogenous degrees and locations of chemotherapeutic drug loading (pg. 351, Abstract). Zimmerman teaches that stochastic conjugation affects the stability of the chemotherapeutic conjugate, as well as potentially, the efficacy, safety, pharmacokinetics, and immunogenicity of ADCs (pg. 351, Abstract).
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have modified the lysate and reaction mixture rendered obvious above, such that they comprise a suppressor tRNA taught by Zimmerman. It would have amounted to combining known lysate and reaction mixture with a known suppressor tRNA, by known means to yield predictable results. A skilled artisan would have had a reasonable expectation of success because both Yin and Zimmerman teach lysates prepared from E. coli which are used in an open cell free synthesis (OCFS) system to produce antibodies, e.g., Trastuzumab, and Zimmerman teaches that an OCFS lysate can be combined with an nnAA incorporation system comprising a suppressor tRNA constitutively expressed from a plasmid. A skilled artisan would have been motivated to combine the lysate and reaction mixture with a suppressor tRNA because Zimmerman demonstrates the combination can be used to produce ADCs, e.g., Trastuzumab-monomethyl auristatin, which are FDA-approved drugs with clinical relevance, and strongly suggests that ADCs produced with nnAAs have improved stability and therapeutic properties due to site-specific drug conjugation.
Response to Remarks - § 103
Applicant’s arguments with respect to the § 103 rejections raised in the prior action have been thoroughly reviewed. Applicant submits that “the intact cells used to produce the whole cell lysate of the instant claims were previously acknowledged as non-obvious in the parent application 15/319,513 (issued as U.S. Patent No. 10,316,322; the ‘322 patent”).” Applicant submits that “the claimed whole cell lysate was also acknowledged as non-obvious because it contains all the components found within the cells of the ‘322 patent.” These arguments are not found convincing. The instant claims are directed to a whole cell lysate, which is a distinct product from “the intact cells… in the parent application… [which] issued as… the ‘322 patent.” The patentability of the parent claims have no bearing on the examination of the instant claims, which are directed to a distinct product.
Applicant also submits that the obviousness rejections should be withdrawn because “the indefiniteness concerns of claim 35” are “fully addressed.” Examiner has withdrawn the § 112(b) rejections raised in the prior action as described above. However, the whole cell lysate as interpreted herein remains obvious over the prior art for the reasons described above. Applicant’s remarks do not address any matter of substance which is relevant to the rejections which are maintained above, with modification necessitated by Applicant’s amendments.
Nonstatutory Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
U.S. Patents
Claims 35, 39-44, and 46-54 are rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of the following U.S. Patents in view of Yin (Yin et al., 1 March 2012, Landes Bioscience, mAbs, 4:2, p. 217-225; of record) as evidenced by Zawada (Zawada et al., 17 February 2011, Biotechnology and Bioengineering, Vol. 108, Issue 7, and Supporting Materials; of record) in view of Dong (Dong et al., April 2010, Applied and Environmental Microbiology, p. 2295-2303; of record). Claims 39 and 46 are in further view of Zimmerman (Zimmerman et al., 17 January 2014, Bioconjugate Chemistry, 25, p. 351-361; of record). Although the claims at issue are not identical, they are not patentably distinct from each other for the reasons that follow. The rejections that follow are maintained from the prior action with modification necessitated by Applicant’s amendments.
Claims 16-23 of Patent No. 10,316,322 B2 – The claims are directed to a method for preparing a whole cell lysate for use in an in vitro protein expression reaction, comprising culturing E. coli cells with the instantly claimed features (an inactivated glnA gene, an auxotrophic selection plasmid constitutive expressing glnA, and a double rate less than 60 minutes), and lysing the cells to prepare the extract. The claims also recite that the auxotrophic selection plasmid comprises one of the instantly claimed chaperone proteins, and a suppressor tRNA.
Claims 1-20 of Patent No. 10,190,145 B2 – The claims are directed to a bacterial cell free synthesis system and methods of using the system, wherein the system comprises a cell free S30 extract of E. coli having an active oxidative phosphorylation system, containing biologically functioning tRNA, amino acids and ribosomes necessary for cell free protein synthesis, a nucleic acid encoding a protein of interest, and wherein the bacteria expressed genes encoding protein chaperones (“disulfide isomerase and a prolyl isomerase”). The claims recite that the protein chaperones may be the instantly claimed chaperones. The claims recite that the protein of interest is an antibody or antibody fragment.
Claims 1-29 of Patent No. 10,774,354 B2 – The claims are directed to a bacterial cell free synthesis system and methods of using the system. The system comprises a cell free S30 extract of E. coli having an active oxidative phosphorylation system, containing biologically functioning tRNA, amino acids and ribosomes necessary for cell free protein synthesis. The system also comprises a nucleic acid encoding a protein of interest, and protein chaperones (“disulfide isomerase and a prolyl isomerase”). The claims recite that the protein chaperones may be the instantly claimed chaperones. The claims recite that the protein of interest is an antibody or antibody fragment.
Claims 6-7 of Patent No. 9,650,621 B2 – The claims are directed to a cell free synthesis system comprising a reaction mixture with “components from a bacterial lysate sufficient to translate a nucleic acid template encoding a protein,” a nucleic acid template encoding a protein of interest and having an amber codon, a tRNA complementary to the amber codon, and a mutant RF1 protein. The claims also recite that the reaction mixture comprises a nnAA, and a corresponding amino acid tRNA synthetase capable of charging the tRNA complementary to the amber codon with the nnAA (i.e., the tRNA therein is a suppressor tRNA).
Claims 7-9 of Patent No. 10,450,353 B2 – The claims are directed to a cell free synthesis system comprising a reaction mixture with “components from a bacterial lysate sufficient to translate a nucleic acid template encoding a protein,” a nucleic acid template encoding a protein of interest and having an amber codon, a tRNA complementary to the amber codon, and a mutant RF1 protein. The claims also recite that the reaction mixture comprises a nnAA, a corresponding amino acid tRNA synthetase capable of charging the tRNA complementary to the amber codon with the nnAA (i.e., the tRNA is a suppressor tRNA), and an active oxidative phosphorylation system that generates ATP.
Claims 5-8 of Patent No. 9,988,619 B2 – The claims are directed to a cell free protein synthesis system comprising a cell free extract of bacteria having biologically functioning tRNA, amino acids, and ribosomes necessary for cell free protein synthesis. The system also comprises a polynucleotide having a coding region encoding the protein of interest and a suppression codon, and a tRNA complementary to the suppression codon in the protein of interest (i.e., a suppressor tRNA). The claims also recite that extract may have an active oxidative phosphorylation system. The protein of interest may be an antibody or antibody fragment. The claims also recite a method of cell-free protein synthesis that comprises mixing a whole cell lysate comprising the aforementioned components with the polynucleotide, and suppressor tRNA.
Claims 5-8 of Patent No. 10,179,909 B2 - The claims are directed to a cell free protein synthesis system comprising a cell free extract of bacteria having biologically functioning tRNA, amino acids, and ribosomes necessary for cell free protein synthesis. The system also comprises a polynucleotide having a coding region encoding the protein of interest and a suppression codon, and a tRNA complementary to the suppression codon in the protein of interest (i.e., a suppressor tRNA). The claims recite that the extract may have an active oxidative phosphorylation system. The protein of interest may be an antibody or antibody fragment. The claims also recite a method of cell-free protein synthesis that comprises mixing a whole cell lysate comprising the aforementioned components with the polynucleotide, and suppressor tRNA.
Claims 9-22 of Patent No. 9,938,516 B2 – The claims are directed to a cell free protein synthesis system comprising a cell free extract of bacteria having biologically functioning tRNA, amino acids, and ribosomes necessary for cell free protein synthesis. The system also comprises a polynucleotide having a coding region encoding the protein of interest and a suppression codon, and a tRNA complementary to the suppression codon in the protein of interest (i.e., a suppressor tRNA). The claims recite that the extract may have an active oxidative phosphorylation system. The protein of interest may be an antibody or antibody fragment. The claims recite a method of cell-free protein synthesis that comprises mixing a whole cell lysate comprising the aforementioned components with the polynucleotide and suppressor tRNA, wherein the extract may have an active oxidative phosphorylation system, and the protein of interest may be an antibody or antibody fragment.
Claims 1-19 of Patent No. 10,648,010 B2 – The claims are directed to a freeze-dried bacterial extract for cell free protein synthesis, and a method of stabilizing the extract. The extract comprises “dried, lysed bacterial components,” wherein the extract is able to synthesize upon rehydration ATP and a target protein from a template nucleic acid encoding the target protein. The claims recite that the extract comprises an active oxidative phosphorylation system.
Claims 1-10 of Patent No. 11,408,021 B2 – The claims are directed to a method of stabilizing a freeze-dried bacterial extract for cell free protein synthesis, wherein the extract comprises lysed bacterial components that enable the extract to synthesize a target protein from a template nucleic acid encoding the target protein in cell free protein synthesis. The claims recite that the extract may be from an Escherichia species and may comprise an active oxidative phosphorylation system.
Claims 1-22 of Patent No. 10,487,133 B2 – The claims are directed to a combination of a nucleic acid template encoding a protein of interest and a cell free protein synthesis system. The claims are also directed to a method of producing a protein of interest by combining the template with the cell free synthesis system and incubating the combination under conditions permitting the translation of the protein of interest. The claims recite the system is derived from a bacterial cell, which may be an E. coli cell. The claims recite the system has an active oxidative phosphorylation system.
Claims 1-28 of Patent No. 12,098,406 B2 (previously identified as co-pending Application No. 17/852,951) – The claims are directed to a freeze-dried bacterial extract for cell free protein synthesis, and a method of producing a target protein comprising mixing the extract with a template nucleic acid encoding the target protein and synthesizing the target protein under conditions that support a cell free protein synthesis reaction. The extract comprises “dried, lysed bacterial components, wherein the extract is able to synthesize upon rehydration a target protein from a template nucleic acid encoding the target protein.” The extract may also have an active oxidative phosphorylation system and may be derived from an Escherichia species.
Claims of 15-16 of Patent No. 12,398,197 (previously identified as co-pending Application No. 17/387,223) – The claims are directed to a method of producing an antibody in a cell-free system, wherein the cell-free system utilizes an extract from E. coli.
The patented claims of I-XIII above, while reciting a generic bacterial cell lysate and/or reaction mixture capable of synthesizing a target protein in a cell-free synthesis reaction, or reciting one or more of the instantly claimed lysate components, do not recite each of the specific components of the instantly claimed lysate and reaction mixture, including “an RNA polymerase that recognizes the promoter operably linked to the gene of interest” in the template nucleic acid (i.e., as in instant claims 37, 44, 52), “a chaperone protein” wherein the chaperone protein is DsbC (i.e., as in instant claims 40-41, 47-48).
The patented claims of I, IV-V, and IX-XII above, while reciting a generic target protein of interest, do not recite that the target protein of interest is an antibody or IgG (i.e., as in instant claim 54).
The patented claims of I-III, and IX-XIII above do not recite that the lysate and reaction mixture comprise a suppressor tRNA (i.e., as in instant claims 39 and 46).
The teachings of Yin, Zawada, Dong, and Zimmerman are recited above and applied hereinafter.
Regarding the specific components of the instantly claimed lysate and reaction mixture, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have included each element of the lysate and reaction mixture of Yin as evidenced by Zawada in view of Dong, in the lysates, reaction mixtures, and cell-free protein synthesis systems of the patented claims. It would have amounted to including known elements of bacterial cell lysates and reaction mixtures used for cell-free protein synthesis, by known means, to yield predictable results. A skilled artisan would have had a reasonable expectation of success that the elements would result in a functional lysate and reaction mixture because Yin teaches the elements of a lysate and reaction mixture for cell-free protein synthesis and uses the elements to produce proteins of interest, and Dong provides a potentially advantageous auxotrophic selection system to adapt the plasmid in Yin’s lysate. A skilled artisan would have been motivated to include the elements because the elements were well-known elements of a cell-free synthesis system, and with respect to the auxotrophic selection plasmid, a known, and potentially advantageous selection method for the “large-scale production of plasmid DNA” in the method of Yin as evidenced by Zawada.
Regarding the instantly claimed protein of interest (antibody), it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have substituted the generic target protein of the patented claims for an antibody taught by Yin. It would have amounted to a simple substitution of known elements, by known means, to yield predictable results. A skilled artisan would have had a reasonable expectation of success in substituting the proteins because the cited prior art uses systems substantially identical to the patented systems to produce antibodies. A skilled artisan would have been motivated to substitute the proteins because antibodies have therapeutic uses, as evidenced by Yin.
Regarding the instantly claimed suppressor tRNA, the obviousness of combining the patented lysates and reaction mixtures with a suppressor tRNA taught by Zimmerman is described in paragraph 25 and applied here.
Co-pending Applications
Claims 35, 39-44, and 46-54 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of the following co-pending Applications in view of Yin (Yin et al., 1 March 2012, Landes Bioscience, mAbs, 4:2, p. 217-225; of record) as evidenced by Zawada (Zawada et al., 17 February 2011, Biotechnology and Bioengineering, Vol. 108, Issue 7, and Supporting Materials; of record) in view of Dong (Dong et al., April 2010, Applied and Environmental Microbiology, p. 2295-2303; of record). Claims 39 and 46 are in further view of Zimmerman (Zimmerman et al., 17 January 2014, Bioconjugate Chemistry, 25, p. 351-361; of record). Although the claims at issue are not identical, they are not patentably distinct from each other for the reasons that follow. These are provisional nonstatutory double patenting rejections because the patentably indistinct claims have not in fact been patented. The rejections that follow are maintained from the prior action with modification necessitated by Applicant’s amendments.
Claims 52-58 of Application No. 16/991,607 – The claims are directed to a bacterial cell-free synthesis system and methods of using the system. The system comprises a cell-free extract prepared from a bacterial strain expressing exogenous protein chaperones, wherein the extract has an active oxidative phosphorylation system, and comprises biologically functioning tRNA, amino acids, ribosomes necessary for cell-free protein synthesis, the exogenous protein chaperones, and a nucleic acid encoding a protein of interest. The claims also recite that the exogenous protein chaperones are DsbC and FkpA.
Claims 1, 5, 14-17, 19, 21, 30, 33-34, 40-41, 43-44, 48-49, 51-53 of Application No. 17/473,544 – The claims are directed to I) a cell-free protein synthesis system comprising a whole cell lysate, and II) a reaction mixture comprising the extract and a nucleic acid encoding a protein of interest (a heavy chain (HC) polypeptide of an antibody), and III) methods of producing an antibody using a cell-free protein synthesis reaction mixture. The claims recite that the synthesis system is derived from an E. coli strain and comprises ribosomes, ATP, amino acids, tRNAs, an oxidative phosphorylation reaction producing ATP, and a chaperone protein, wherein the chaperone protein may be one of the instantly recited chaperone proteins. The method further comprises incorporating at least one nnAA in the protein of interest (i.e., the HC).
Claims 1-5, 49, 51, 53, 93-97, 117-120, 125 of Application No. 18/231,204 – The claims are directed to a spray-dried bacterial extract for cell-free protein synthesis comprising “dried, lysed bacterial components,” wherein upon rehydration the extract is able to synthesize a target protein from a template nucleic acid encoding the target protein. The claims are also directed to a method of producing a target protein comprising combining the spray-dried bacterial extract with a template nucleic encoding a target protein.
The co-pending claims of I-III above, while reciting a generic bacterial cell lysate and/or reaction mixture capable of synthesizing a target protein in a cell-free synthesis reaction, or reciting one or more of the instantly claimed lysate components, do not recite each of the specific components of the instantly claimed lysate and reaction mixture. The obviousness of including the specific elements of the lysate and reaction mixture taught by Yin as evidenced by Zawada in view of Dong, is described above in paragraph 32 and applied here.
The co-pending claims of I and III above, while reciting a generic target protein of interest, do not recite that the target protein of interest is an antibody or IgG. The obviousness of substituting the generic protein of the co-pending claims for an antibody taught by Yin is described in paragraph 33 and applied here.
The co-pending claims of I-III above do not recite that the lysates and reaction mixtures comprise a suppressor tRNA. The obviousness of combining the co-pending lysates and reaction mixtures with a suppressor tRNA taught by Zimmerman is described in paragraph 25 and applied here.
Response to Arguments - Nonstatutory Double Patenting
Applicant’s remarks regarding the nonstatutory double patenting rejections raised in the prior action have been considered. Examiner acknowledges Applicant’s request that the double patenting rejections be reconsidered in view of the claim amendments and remarks. The scope of the amended claims and patented and co-pending claims have been considered. Applicant’s amendments are insufficient to distinguish the instant claims from the patented and co-pending claims in view of Yin as evidenced by Zawada, Dong, and Zimmerman. The rejections remain outstanding.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/JENNA L PERSONS/Examiner, Art Unit 1637
/Soren Harward/Primary Examiner, TC 1600
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